I managed to find this:
It's snippets from Bad Name, LOAP and It's My Life. It seems like the talkbox was malfunctioning throughout.

Has someone an idea about the history of the prayer chorus backing vocals.

During the SWW tour they used the original recording for the chorus due to Jons voice problems.
At the New Jersey tour they had a recording that sounded like Jon.
After that until lost highway they used the overpowered backing track which in my opinion is Richie singing.
Then they got rid of this overpowered backing track and changed it to something not so noticeable and even left it out at a lot of concerts completely.
Phil X is capable of singing the Prayer Chorus(in my opinion one of the few things he can) but I have no idea if they are still running a backing track during the chorus.
I could also be wrong with my assumptions.
Any ideas about the history of the prayer backing vocals?

As to your point about some shows not having any backing track at all, is that the case? To me it's always been there but it's possible people have heard otherwise.

It's complicated. In 1986, the early stages of the SWW tour, there are numerous gigs in which Jon sings the high notes in the chorus and the key change as well. After the vocal problems, they used the vocal tracks from the original album.
During most of the NJ tour, Jon seems like he was protecting his voice on LOAP. There are performances of the song where he doesn't sing any of the high notes, not even the line before the guitar solo. The vocal track used seems to be the one from the SWW album, half a step down of course.
On the Keep The Faith tour, Jon's best vocal period, there were performances where he sung the high notes in the chorus but not the key change. The vocal track they used then Sounds a bit different compared to the original one.
On the These Days tour, there were times where the vocal track wasn't used, and you could only hear the other guys in the band sing the high notes. There was even a concert in 1995, where Jon attempted one of the screams in the key change. The vocal track used, for example in the Wembley DVD, is the original from SWW.
After that, from the Crush tour to the beginning of the Lost Highway tour, they used I think the original vocal track.
For some reason, they dropped the vocal tracks from 2008-13 I don't know why.
And after that, from I think 2016/17, they use the vocal track which they still use now, and I think the voice you hear on the voice track is Phil X.

That's a good point, do they need to rerecord it each time there's a member shakeup?

No, but don't you that it'll be a little dumb to still use the original track from SWW? It sounded weird back in the day when you see Jon pointing the mic to the crowd and you suddenly hear young Jon belting out "woah-oh livin on a prayer".

Thanks for the information.
In the Wembley95 concert recording is also it also the orginal SWW recording after the key change. In my opinion it sounds really different.

One won't believe how many songs have subtle backing tracks in the chorus, I'd say around 80% of the show.
That's quite standard for bands of this size.

The Prayer backing vocals were probably recorded a couple of times by the band throughout the numerous tours. I was sad to see them change it in 2008, the song lost so much power without them.

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80 percent feels high, that's surprising. Wouldn't they need to be playing to a click for all those songs though?

I actually think that they have a click on pretty much every track.

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